2008 GMOD Summer School

The first annual GMOD Summer School will be held July 11-13, 2008 at the National Evolutionary Synthesis Center (NESCent) in Durham, North Carolina. GMOD Summer school is a 2 1/2 day hands-on workshop aimed at teaching new GMOD users how to get up and running with popular GMOD components. There will also be a concurrent 1 day session aimed at principal investigators that will give decision makers a feel for what GMOD can do and what level of resources are needed to get a GMOD installation up and running.

Plans for the GMOD Summer School are still being finalized. Registration will open by mid-March. Please contact the GMOD Help Desk if you have any questions.

Program

The program will feature two tracks:

Implementation Track

Two and half days of hands on training starting with an overview of GMOD and then covering installation and configuration of popular GMOD tools, include Chado, GBrowse, CMap, Apollo, and the Community Annotation System.

Principal Investigator Track

This shorter track (Saturday and Sunday only) will provide an overview of what GMOD can do, how the GMOD community works, and give participants a glimpse of what's involved in getting GMOD tools up and running. In addition to PI-only sessions, participants will be paired with an Implementation Track participant during the Community Annotation System session, so that PIs can get a feel for what is involved in getting GMOD software installed and configured.

A detailed program for both tracks will be posted here by mid-March.

Instructors

Sessions will be taught by experienced GMOD personnel, including:

• Scott Cain - GMOD Project Coordinator
• Dave Clements - GMOD Help Desk
• Ben Faga - CMap (and other GMOD components) developer
• Ed Lee - Apollo developer

Who Should Attend?

The GMOD Summer School has tracks for both the people who implement GMOD at your organization, and for Principal Investigators who would benefit from having their organizations use GMOD.

Implementation Track

The Implementation Track goes into detail about how to install and configure GMOD components. It is aimed at GMOD System Administrators, the people who actually implement and manage a GMOD installation on a day to day basis. This track is for GMOD sys admins from organizations that are either planning to use GMOD components, or are in the early phases of implementing GMOD.

Prerequisites

The Implementation Track requires a minimal level of Linux systems administration knowledge (see Computing Requirements). Attendees without that minimal level of knowledge will likely be lost for most of the course.

By "a minimal level of Liinux systems administration knowledge" we mean that participants should be comfortable installing packages under Linux. A good benchmark for this level of knowledge is that you should be able to get a basic GBrowse installation (that is, GBrowse without MySQL) up and running with the example GBrowse data. This also requires installing Apache, and BioPerl and all its dependencies. This is a non-trivial task for beginning Linux sys admins, but if you can do this successfully then you will likely fully participate in the course. If you can't then the course will be, at best, frustrating for you.

System Requirements

Participants are required to bring their own laptops, and those laptops must already be capable of running a VMware system image.

Each session will start with different VMware image that was built specifically for that session. Some VMware images will incorporate work covered in earlier sessions. For example, the image used in the GBrowse session will already have PostgreSQL and Chado installed and Chado will be preloaded with example data.

VMware on Windows and Linux

A free VMware player is available for Microsoft Windows and Linux operating systems from VMware. You will need to register to download it.

VMware on Mac OS X

There is no free VMware player that runs directly under Mac OS X. However, there are several other options:

Mac OS 10.5 (Leopard) and Boot Camp

The latest release of Mac OS (Leopard) includes Boot Camp, a feature that allows you to boot your Mac into another operating system, include Windows or Linux. From there you can install the VMware player for your OS.*

VMware Fusion

VMware's Fusion product ($79.99) allows you to run Windows or Linux under Mac OS. From there you can install the VMware player for your OS.*

Parallels Desktop for Mac

Another option is Parallels Desktop for Mac ($79.99). Like Fusion, Parallels allows you to run Windows and Linux under Mac OS. And once again, from there you can install the VMware player for your OS.*

*	This is how it is supposed to work anyway! We haven't tested any of these options all the way through yet. We will update this page as we try each.

Principal Investigator Track

The PI Track is geared towards decision makers that are considering using GMOD at their organization. This track introduces participants to what GMOD can do, how the GMOD community works, and offers insight into how GMOD might work at their site. This track does not require any computing skills.

Who should consider using GMOD? If your organization has more data than you can manage using word processors and spreadsheets then you should consider GMOD. GMOD offers an integrated set of tools for common tasks related to biological data. GMOD is particularly attractive to groups that need to manage, visualize and/or annnotate genomic data. GMOD also offers a community of users and developers who support it.

Prerequisites

The only prerequisite for the PI Track is that you have or expect to have more data than you can manage, visualize and annotate using current methods.

Cost and Registration

There is no tuition cost for the GMOD Summer School. It's free. Participants are responsible for their own travel, lodging and meal expenses. Assistance is available for travel and living expenses to participants from underrepresented groups; please contact the GMOD Help Desk for more information.

The Implementation Track is limited to 15 participants; the PI Track is limited to 10 participants.

Registration will open by mid-March. Watch this space.

Location

The GMOD Summer School will be held at the National Evolutionary Synthesis Center (NESCent) in Durham, North Carolina, United States.

Transportation and lodging information will be added here as the course draws nearer.

Acknowledgements

The GMOD Summer School is funded by NIH grant 1R01HG004483-01 under Ian Holmes.